Thermal-response of a protein (hHv1) by a coarse-grained MC and all-atom MD computer simulations

Panisak Boonamnaj, Sunita Subedi Paudel, Warin Jetsadawisut, Sunan Kitjaruwankul, Pornthep Sompornpisut and R.B. Pandey

Physica A: Statistical Mechanics and its Applications, 2019, vol. 527, issue C

Abstract: A Monte Carlo simulation with a coarse-grained (CGMC) model of protein involving a phenomenological residue–residue interaction potential, augmented by a Molecular Dynamics simulation is used to investigate local and global structures of a protein (hHv1) as a function of temperature. Data from both all-atom MD and a coarse-grained MC simulations show that the radius of gyration of the protein (the cytoplasmic domain of hHv1 monomer and dimer) decreases on increasing the temperature, i.e. it becomes more globular on heating in its native phase in contrast to its thermal expansion in denatured phase. The globularization of the protein is quantified by analyzing the scaling of the structure factor. The crossover from globular to random-coil structure involving segmental reorganizations is found to depend on the length scale and the temperature.

Keywords: Coarse-grained model; Monte Carlo simulation; Molecular Dynamics simulation; Voltage-gated proton channel protein hHv1 (search for similar items in EconPapers)
Date: 2019
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Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:527:y:2019:i:c:s0378437119307757

DOI: 10.1016/j.physa.2019.121310

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